Precise dd excitations and commensurate intersite Coulomb interactions in the dissimilar cuprate YBa_2Cu_3O_(7-x) and La_(2-x)Sr_xCuO_4

Using high-resolution extreme ultraviolet resonant inelastic X-ray scattering (EUVRIXS) spectroscopy at Cu M-edge, we observed the doping dependent spectral shifts of inter-orbital (dd) excitations of YBa_2Cu_3O_(7-x) and La_(2-x)Sr_xCuO_4. With increasing hole doping level from undoped to optimally doped superconducting compositions, the leading edge of dd excitations is found to shift towards lower energy loss in a roughly linear trend that is irrespective to the cuprate species. The magnitude of energy shift can be explained by including a 0.15 eV Coulomb attraction between Cu 3d_(x^2-y^2) electrons and the doped holes on the surrounding oxygens in the atomic multiplet calculations. The consistent energy shift between distinct cuprate families suggests that this inter-site Coulomb interaction energy scale is relatively material-independent, and provides an important reference point for understanding charge density wave phenomena in the cuprate phase diagram.Comment: 29 pages; 8 figures. Physical Review B, in press. This paper reveals a Cu 3d-O 2p intersite interaction energy for the first time experimentally. It also explains why Tc of YBCO is higher than that of LSC

Phenotypic and Transcriptomic Response of Auxotrophic Mycobacterium avium Subsp. paratuberculosis leuD Mutant under Environmental Stress

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of severe gastroenteritis in cattle. To gain a better understanding of MAP virulence, we investigated the role of leuD gene in MAP metabolism and stress response. For this, we have constructed an auxotrophic strain of MAP by deleting the leuD gene using allelic exchange. The wildtype and mutant strains were then compared for metabolic phenotypic changes using Biolog phenotype microarrays. The responses of both strains to physiologically relevant stress conditions were assessed using DNA microarrays. Transcriptomic data was then analyzed in the context of cellular metabolic pathways and gene networks. Our results showed that deletion of leuD gene has a global effect on both MAP phenotypic and transcriptome response. At the metabolic level, the mutant strain lost the ability to utilize most of the carbon, nitrogen, sulphur, phosphorus and nutrient supplements as energy source. At the transcriptome level, more than 100 genes were differentially expressed in each of the stress condition tested. Systems level network analysis revealed that the differentially expressed genes were distributed throughout the gene network, thus explaining the global impact of leuD deletion in metabolic phenotype. Further, we find that leuD deletion impacted metabolic pathways associated with fatty acids. We verified this by experimentally estimating the total fatty acid content of both mutant and wildtype. The mutant strain had 30% less fatty acid content when compared to wildtype, thus supporting the results from transcriptional and computational analyses. Our results therefore reveal the intricate connection between the metabolism and virulence in MAP

Deciphering the Preference and Predicting the Viability of Circular Permutations in Proteins

Circular permutation (CP) refers to situations in which the termini of a protein are relocated to other positions in the structure. CP occurs naturally and has been artificially created to study protein function, stability and folding. Recently CP is increasingly applied to engineer enzyme structure and function, and to create bifunctional fusion proteins unachievable by tandem fusion. CP is a complicated and expensive technique. An intrinsic difficulty in its application lies in the fact that not every position in a protein is amenable for creating a viable permutant. To examine the preferences of CP and develop CP viability prediction methods, we carried out comprehensive analyses of the sequence, structural, and dynamical properties of known CP sites using a variety of statistics and simulation methods, such as the bootstrap aggregating, permutation test and molecular dynamics simulations. CP particularly favors Gly, Pro, Asp and Asn. Positions preferred by CP lie within coils, loops, turns, and at residues that are exposed to solvent, weakly hydrogen-bonded, environmentally unpacked, or flexible. Disfavored positions include Cys, bulky hydrophobic residues, and residues located within helices or near the protein's core. These results fostered the development of an effective viable CP site prediction system, which combined four machine learning methods, e.g., artificial neural networks, the support vector machine, a random forest, and a hierarchical feature integration procedure developed in this work. As assessed by using the hydrofolate reductase dataset as the independent evaluation dataset, this prediction system achieved an AUC of 0.9. Large-scale predictions have been performed for nine thousand representative protein structures; several new potential applications of CP were thus identified. Many unreported preferences of CP are revealed in this study. The developed system is the best CP viability prediction method currently available. This work will facilitate the application of CP in research and biotechnology

The Somatic Genomic Landscape of Glioblastoma

We describe the landscape of somatic genomic alterations based on multi-dimensional and comprehensive characterization of more than 500 glioblastoma tumors (GBMs). We identify several novel mutated genes as well as complex rearrangements of signature receptors including EGFR and PDGFRA. TERT promoter mutations are shown to correlate with elevated mRNA expression, supporting a role in telomerase reactivation. Correlative analyses confirm that the survival advantage of the proneural subtype is conferred by the G-CIMP phenotype, and MGMT DNA methylation may be a predictive biomarker for treatment response only in classical subtype GBM. Integrative analysis of genomic and proteomic profiles challenges the notion of therapeutic inhibition of a pathway as an alternative to inhibition of the target itself. These data will facilitate the discovery of therapeutic and diagnostic target candidates, the validation of research and clinical observations and the generation of unanticipated hypotheses that can advance our molecular understanding of this lethal cancer

Hazardous Wastes Treatment Technologies

A review of the literature published in 2017 on topics relating to hazardous waste management in water, soils and air. This review covers hazardous waste treatment theologies and applying physical, chemical, and biological principles

Nanomaterial powders and deposits prepared by flame spray processing of liquid precursors

Ultrafine grained Al2O3, Mn2O3, ZrO2 and Y2O3-ZrO2 powders and deposits were produced by flame spray processing of atomized precursor solutions. Ceramic particles of 1-150nm size were collected on an electrostatic precipitator at a rate of ~5-20 mglmin, with ~5-25% collection efficiency. Nanograined oxide deposits with a powder morphology were produced at a deposition efficiency of < 10%. The spray feedstock and processing conditions affected the size, shape and phase composition of the synthesized nanomaterials. Particles with wider distributions of larger size grains were produced from aqueous solutions, whereas narrow range of fine-grained material was produced from organo-metallic precursors. Liquid flame spraying is a viable technique to produce nanoparticles and deposits

Nonporous silicone polymer coating of expanded polytetrafluoroethylene grafts reduces graft neointimal hyperplasia in dog and baboon models

AbstractPurpose: Neointimal hyperplasia frequently develops after placement of prosthetic vascular grafts and is a major cause of graft failure. This study was an attempt to prevent vascular lesion formation by coating the graft luminal surface with a thin layer of nonporous silicone polymer, and subsequently with an ultrathin layer of vapor phase (plasma gas) deposited fluoropolymer, thereby providing a smooth and chemically uniform surface that was postulated to limit pannus tissue ingrowth across the graft anastomoses.Methods: Bilateral femoral arteriovenous (AV) conduits were constructed in four dogs using expanded polytetrafluoroethylene graft materials (ePTFE; 6-mm inside diameter, 2.5-cm long). In each animal, one femoral AV shunt was constructed from a graft whose luminal surface was entirely coated with polymer. On the contralateral side, an uncoated graft served as a control. Bilateral aortoiliac grafts were placed in three baboons using 5-cm segments of ePTFE (4-mm inside diameter). One end (1 cm) of each graft had been coated with polymer. In each animal, the coated end of one graft was placed proximally and the coated end of the second graft was placed distally in the contralateral vessels.Results: All grafts were patent at 30 days. In the dog model, there was a significant reduction in graft neointimal area at the venous anastomoses for the coated grafts compared with the uncoated grafts (0.03 ± 0.02 mm 2 and 1.11 ± 0.54 mm 2 , respectively; p < 0.05). In the baboon model, the silicone coating significantly reduced the graft neointimal thickness (0.003 ± 0.003 mm vs 0.21 ± 0.05 mm; p < 0.05) and neointimal area (0.05 ± 0.08 mm 2 vs 0.82 ± 0.58 mm 2 ; p < 0.05).Conclusions: These data demonstrate that healing of ePTFE grafts can be effectively modified by altering the physical properties of the graft surface. Neointimal hyperplasia within ePTFE grafts is significantly reduced by the local application of a fluorocarbon-coated, silicone-based polymer. The resulting graft flow surface effectively prevents tissue ingrowth from the adjacent native vessel, thereby preserving the anastomosis luminal area. This approach could represent a new strategy for limiting graft surface anastomotic neointimal hyperplasia. (J Vasc Surg 1996;24:825-33.